Dear Modeller
I was using the script Align2D.top below to run modeller with version
6.2. Now that we installed version 7, I just can't get it to
work. I get the following message:
read_al_375E> Unknown residue type,position,sequence: 1 2
recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
Could you please let me know what is wrong?
Thanks,
Paula Kuser
Align2D.top
#############################################
# ALIGNING OUR TARGET WITH THE TEMPLATE
#
# file.pdb - your template pdb file
# pdb name - template code
# seq.txt - target file in pir format
# seq - target code
# file.ali - constructed alignment file
#############################################
# Include MODELLER library scripts
#INCLUDE
# Defining our local pdb directory for input
#SET ATOM_FILES_DIRECTORY = '/db/pdb'
# Reading template pdb file
READ_MODEL FILE = '1ig8.pdb'
# Defining code of the template
SEQUENCE_TO_ALI ALIGN_CODES = '1ig8'
# Reading our target
READ_ALIGNMENT FILE = 'seq.txt', ALIGN_CODES = ALIGN_CODES 'HEX',
ADD_SEQUENCE = on
# Alignment
ALIGN2D
# Alignment in pir formate
WRITE_ALIGNMENT FILE='HEXTC.ali', ALIGNMENT_FORMAT = 'PIR'
Here is the seq.txt file:
#########################################################
#
#TARGET SEQUECE IN PIR FORMAT
#
###########################################
>P1;HEX
sequence:HEX:.:.:.:.
MSARLNNLLQHIAVKDKDSDTMRHLKQRMALASLANQFTVGKDHLKQLMLYMVHQMIEG
LEGRESTLRMLPSYVYKTDPSKATGVFYALDLGGTNFRVLRVTCKEGRVADRVDAKFVI
PQQALQGTAEDLFGFIAQSVKKMMEQKAPEDLNRTVPLGFTFSFPTEQKGVDHGFLIKW
TKGFSTRGVEGKDVVELLQKALKRMEVKVKVVALCNDTVGTLITNYFFDPDTQVGVIIG
TGSNACYFEDAYAVTKEPSVAARGTTQTPINMECGNFDSKYKFVLPVTAYDEAMDAVTP
NRNFQTQEKMVSGMYLGEISRRMIAHLAELHCLPSALASKMAKPWSFETKFMGMISADR
MPGLQFTRQVFQELFQVDVTDVADLHVIRDVCCLVRGRAAQISAMFCSAPLVKTRKEGR
ATVAIDGSVFEKTPSFRRLLQQNMNAILGPGCDVTTALARDGSGIGAAFISALVVNDK*
Paula Kuser Falcão
Laboratório de Bioinformática Estrutural
Embrapa Informática Agropecuária
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